KEGG   PATHWAY: savi00020
Entry
savi00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Shewanella avicenniae
Description
The citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form of acetate, derived from glycolysis and pyruvate oxidation for carbohydrates and from beta oxidation of fatty acids. The two-carbon acetyl group in acetyl-CoA is transferred to the four-carbon compound of oxaloacetate to form the six-carbon compound of citrate. In a series of reactions two carbons in citrate are oxidized to CO2 and the reaction pathway supplies NADH for use in the oxidative phosphorylation and other metabolic processes. The pathway also supplies important precursor metabolites including 2-oxoglutarate. At the end of the cycle the remaining four-carbon part is transformed back to oxaloacetate. According to the genome sequence data, many organisms seem to lack genes for the full cycle [MD:M00009], but contain genes for specific segments [MD:M00010 M00011].
Class
Metabolism; Carbohydrate metabolism
Pathway map
savi00020  Citrate cycle (TCA cycle)
savi00020

Module
savi_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:savi00020]
savi_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:savi00020]
savi_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:savi00020]
savi_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:savi00020]
Other DBs
GO: 0006099
Organism
Shewanella avicenniae [GN:savi]
Gene
JYB87_11490  citrate synthase [KO:K01647] [EC:2.3.3.1]
JYB87_01860  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
JYB87_10415  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
JYB87_05855  isocitrate dehydrogenase [KO:K00030] [EC:1.1.1.41]
JYB87_11465  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
JYB87_11460  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
JYB87_01835  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
JYB87_11450  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
JYB87_11455  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
JYB87_11475  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
JYB87_11470  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
JYB87_11485  sdhC; succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
JYB87_11480  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
JYB87_14765  frdA; fumarate reductase (quinol) flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
JYB87_14760  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
JYB87_14755  frdC; fumarate reductase subunit FrdC [KO:K00246]
JYB87_14750  frdD; fumarate reductase subunit FrdD [KO:K00247]
JYB87_16390  fumarate reductase flavoprotein subunit [KO:K00233] [EC:1.3.5.1 7.1.1.12]
JYB87_16385  fumarate reductase iron-sulfur subunit [KO:K25995] [EC:1.3.5.1 7.1.1.12]
JYB87_16400  fumarate reductase cytochrome b subunit [KO:K25996]
JYB87_16395  fumarate reductase cytochrome b subunit [KO:K25996]
JYB87_03940  flavocytochrome c [KO:K26318] [EC:1.3.2.4]
JYB87_02935  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
JYB87_09450  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
JYB87_14265  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
JYB87_14505  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
JYB87_14510  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
JYB87_02955  acetyl-CoA carboxylase biotin carboxylase subunit [KO:K01959] [EC:6.4.1.1]
JYB87_02960  oadA; sodium-extruding oxaloacetate decarboxylase subunit alpha [KO:K01960] [EC:6.4.1.1]
JYB87_01825  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
JYB87_01830  aceF; dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
Compound
C00022  Pyruvate
C00024  Acetyl-CoA
C00026  2-Oxoglutarate
C00036  Oxaloacetate
C00042  Succinate
C00068  Thiamin diphosphate
C00074  Phosphoenolpyruvate
C00091  Succinyl-CoA
C00122  Fumarate
C00149  (S)-Malate
C00158  Citrate
C00311  Isocitrate
C00417  cis-Aconitate
C05125  2-(alpha-Hydroxyethyl)thiamine diphosphate
C05379  Oxalosuccinate
C05381  3-Carboxy-1-hydroxypropyl-ThPP
C15972  Enzyme N6-(lipoyl)lysine
C15973  Enzyme N6-(dihydrolipoyl)lysine
C16254  [Dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine
C16255  [Dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine
Reference
  Authors
Nishizuka Y (ed).
  Title
[Metabolic Maps] (In Japanese)
  Journal
Tokyo Kagaku Dojin (1980)
Reference
  Authors
Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).
  Title
[Cellular Functions and Metabolic Maps] (In Japanese)
  Journal
Tokyo Kagaku Dojin (1997)
Reference
  Authors
Michal G.
  Title
Biochemical Pathways
  Journal
Wiley (1999)
Related
pathway
savi00010  Glycolysis / Gluconeogenesis
savi00053  Ascorbate and aldarate metabolism
savi00061  Fatty acid biosynthesis
savi00071  Fatty acid degradation
savi00190  Oxidative phosphorylation
savi00220  Arginine biosynthesis
savi00250  Alanine, aspartate and glutamate metabolism
savi00280  Valine, leucine and isoleucine degradation
savi00350  Tyrosine metabolism
savi00470  D-Amino acid metabolism
savi00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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